The three Dragons that Link encounters in his quest resemble the three Great Fairies from Ocarina of Time. These Great fairies have been in other games, such as The Wind Waker and Majora's Mask, but the Dragons have been adapted to look mainly like the Great Fairies in their first appearance that is Ocarina of Time.

Both the Kikwi Hermit in Faron Woods and the Parella in the cave with all of the breakable walls in Lake Floria that tells you where the exit is say: "It's a secret to everybody.". This is the same line rupee-paying Moblins used in The Legend of Zelda.

When asked to deliever a letter from Cawlin, you will be given the opporitunity to instead hand it over to the hand coming out of a toilet in need of paper. This is a reference to the hand coming out of the toilet in the Clocktown Inn from Majora's Mask.